Hi Tsjerk,
>Hi Akansha,
>Either you need to simulate both systems until you
>have full
>convergence before you can make conclusions regarding
>the (dis)similar behaviour
Well I can simulate it until convergence but that on a
single processor for my system will take several
months of computer time.
>or you have to test consistently, running replicate
>simulations both on one processor and on 16.
This is what I was doing. I was running exactly
identical simulations on 1 processor and on 16
processors.
By identical i mean - same starting structure,
velocities taken from the same *.trr file. The only
difference was the number of nodes for the production
run.
>That being said, it is very well possible that even
>between two
>simulations of the same system under completely
>identical conditions,
>except for the starting velocities and possibly the
>exact starting
>structure, you will get two completely different
>results. If you're
>protein can undergo a conformational change it's
>basically a matter of
>chance whether you observe it or not.
But I give the same velocities and use exactly same
starting structure for both simulations. Basically I
use the same files for both cases. Only difference
lying in the number of processors.
I would think that with same intial conditions the
calculations should be identical for both cases.
>Of course, I don't say it is not related to your
>simulation being
>distributed over multiple processors. It may be, but
>in order to
>exclude other effects you have to repeat simulations
>and/or work
>through the code very carefully. Which version of
>Gromacs did you use?
I am using Gromacs3.3.
It would very helpful if you can please suggest what
care should I take in order to exclude other effects
when I repeat the simulation.
Thanx
Akansha
>Hope it helps,
>>Tsjerk
>On 9/18/06, Akansha Saxena <asaxena17 at yahoo.com>
>wrote:
>> Hello
>>>> Has anybody seen a protein becoming unstable on
>> parallel nodes while remaining stable on single
>>node?
>>>> I am running a NPT molecular dynamics simulation.
>>The system contains a protein with 141 residues
>>surrounded
>> by water making the total to 32714 atoms. I ran
this
>> simulation at two places for 8ns. One as a serial
>>job
>> and the other as a parallel job on 16 nodes.
>>>> The protein remains stable all through for the
>>serial
>> job but for parallel job the protein opens up
after
>> 3ns of simulation and is never stable after that.
>>>> All other conditions are exactly the same. Any help
>> would be highly appreciated.
>>>> Akansha
>>>>>>>> Akansha Saxena
>> Graduate Student
>> Department of Biomedical Engineering
>> Washington University in St Louis
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>--
>Tsjerk A. Wassenaar, Ph.D.
>Groningen Biomolecular Sciences and Biotechnology
>Institute (GBB)
>Dept. of Biophysical Chemistry
>University of Groningen
>Nijenborgh 4
>9747AG Groningen, The Netherlands
>+31 50 363 4336
Akansha Saxena
Graduate Student
Department of Biomedical Engineering
Washington University in St Louis
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